Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe · Michael R. Crusoe
--- a/.github/ISSUE_TEMPLATE.md
+++ b/.github/ISSUE_TEMPLATE.md
-To help us debugging your issue, please make sure you
+:exclamation: Make to check out our [User Guide](https://github.com/soedinglab/hh-suite/wiki).

- [ ] included the HHsuite version or commit ID
- [ ] added information about your operating system and compiler (if building from source)
- [ ] checked the [user-guide](https://github.com/soedinglab/hh-suite/blob/master/hhsuite-userguide.pdf) for available documentation
- [ ] ideally also included a minimal example for us to reproduce the issue
+## Expected Behavior
+
+## Current Behavior
+
+## Steps to Reproduce (for bugs)
+Please make sure to execute the reproduction steps.
+
+## HH-suite Output (for bugs)
+Please make sure to post the complete output of the tool you called. Please use [gist.github.com](https://gist.github.com).
+
+## Context
+Providing context helps us come up with a solution and improve our documentation for the future.
+
+## Your Environment
+Include as many relevant details about the environment you experienced the issue in.
+* Version/Git commit used:
+* Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
+* Operating system and version:
--- a/.gitmodules
+++ b/.gitmodules
-[submodule "lib/ffindex"]
-	path = lib/ffindex
-	url = https://github.com/soedinglab/ffindex_soedinglab.git
--- a/.travis.yml
+++ b/.travis.yml
-# Ubuntu 14.04 Trusty support
-sudo: required
-dist: trusty
-
-addons:
-  apt:
-    packages:
-    - cmake
-
-before_install:
- git submodule update --init --recursive
+language: minimal

 script:
  - mkdir build
  - cd build
- cmake .. && make
- CTEST_OUTPUT_ON_FAILURE=TRUE make test
+  - cmake $CMAKE_EXTRA .. && make -j $(nproc --all || sysctl -n hw.ncpu)
+  - |
+    if [[ "$CMAKE_EXTRA" != "" ]]; then \ 
+        make install; \
+        export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"; \
+        (cd ../data && ./test.sh); \
+    fi

+before_install:
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew link gcc@8 --force; fi
+  - export CC
+  - export CXX

 matrix:
  include:
-    - compiler: gcc
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
          packages:
-            - g++-4.9
+            - cmake
+            - gcc-4.8
+            - g++-4.8
            - mpi-default-dev
-      env: CXX=g++-4.9
-    - compiler: gcc
+      env: CC=gcc-4.8 CXX=g++-4.8
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
          packages:
-            - g++-5
+            - cmake
+            - g++-8
            - mpi-default-dev
-      env: CXX=g++-5
-    - compiler: gcc
+      env: CC=gcc-8 CXX=g++-8
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
          packages:
-            - g++-6
+            - cmake
+            - g++-8
+            - mpi-default-bin
            - mpi-default-dev
-      env: CXX=g++-6
-    - compiler: gcc
+      env: CC=gcc-8 CXX=g++-8 CMAKE_EXTRA="-DENABLE_SANITIZERS=1 -DCMAKE_BUILD_TYPE=ASan -DCMAKE_INSTALL_PREFIX=."
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
+            - llvm-toolchain-precise-3.6
          packages:
-            - g++-7
+            - cmake
+            - clang-3.6
            - mpi-default-dev
-      env: CXX=g++-7
-    - compiler: clang
+      env: CC=clang-3.6 CXX=clang++-3.6
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
-            - llvm-toolchain-precise-3.6
+            - llvm-toolchain-trusty-7
          packages:
-            - clang-3.6
+            - clang-7
+            - libc++-7-dev
+            - libc++abi-7-dev
            - mpi-default-dev
-      env: CXX=clang++-3.6
-    - compiler: clang
+      env: CC=clang-7 CXX=clang++-7
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
-            - llvm-toolchain-precise-3.7
          packages:
-            - clang-3.7
-            - mpi-default-dev
-      env: CXX=clang++-3.7
-    - compiler: clang
+            - cmake
+            - gcc-4.8
+            - g++-4.8
+      env: CC=gcc-4.8 CXX=g++-4.8
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
-            - llvm-toolchain-precise-3.8
          packages:
-            - clang-3.8
-            - mpi-default-dev
-      env: CXX=clang++-3.8
-    - compiler: clang
+            - cmake
+            - g++-8
+      env: CC=gcc-8 CXX=g++-8
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
-            - llvm-toolchain-trusty-3.9
+            - llvm-toolchain-precise-3.6
          packages:
-            - clang-3.9
-            - mpi-default-dev
-      env: CXX=clang++-3.9
-    - compiler: clang
+            - cmake
+            - clang-3.6
+      env: CC=clang-3.6 CXX=clang++-3.6
+    - os: linux
+      dist: trusty
      addons:
        apt:
          sources:
            - ubuntu-toolchain-r-test
-            - llvm-toolchain-trusty-4.0
+            - llvm-toolchain-trusty-7
          packages:
-            - clang-4.0
-            - mpi-default-dev
-      env: CXX=clang++-4.0
+            - clang-7
+            - libc++-7-dev
+            - libc++abi-7-dev
+      env: CC=clang-7 CXX=clang++-7
+    - os: osx
+      osx_image: xcode10.1
+      addons:
+        homebrew:
+          packages:
+            - cmake
+            - gcc@8
+      env: CC=gcc-8 CXX=g++-8
--- a/CHANGES
+++ b/CHANGES
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
 cmake_minimum_required(VERSION 2.8.12)
-project(hhsuite CXX)
-
-SET(HAVE_SSSE3 0 CACHE BOOL "Have SSSE3")
-SET(HAVE_AVX2 0 CACHE BOOL "Have AVX2")
-
-#set(CMAKE_BUILD_TYPE Release)
-
-# find compiler
-if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-  message("-- Compiler is clang(++)")
-  set(CMAKE_COMPILER_IS_CLANG 1)
-elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-  message("-- Compiler is GNU ")
-  set(CMAKE_COMPILER_IS_GNUCXX 1)
-  set(CMAKE_COMPILER_IS_GNUCCC 1)
-elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
-  message("-- Compiler is ICC ")
-  set(CMAKE_COMPILER_IS_ICC 1)
+project(hhsuite C CXX)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+
+set(HAVE_SSE2 0 CACHE BOOL "Have SSE2")
+set(HAVE_AVX2 0 CACHE BOOL "Have AVX2")
+set(ENABLE_SANITIZERS 0 CACHE BOOL "Enable Sanitizers")
+
+if (NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release)
+endif (NOT CMAKE_BUILD_TYPE)
+
+if (${ENABLE_SANITIZERS})
+    include(FindUBSan)
+    include(FindASan)
+    include(FindMSan)
+    include(FindTSan)
 endif ()

-
-message("-- Processor is ${CMAKE_SYSTEM_PROCESSOR}")
-
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64.*|x86_64.*|AMD64.*")
-  set(X86_64 1)
-elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "i686.*|i386.*|x86.*|amd64.*|AMD64.*")
-  set(X86 1)
-elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(arm.*|ARM.*)")
-  set(ARM 1)
-elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(aarch64.*|AARCH64.*)")
-  set(AARCH64 1)
-elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "PPC64*|ppc64*|powerpc64*")
-  set(PPC64 1)
-elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "PPC*|ppc*|powerpc*")
-  set(PPC 1)
-endif()
-
-
-
 set(HHSUITE_VERSION_MAJOR 3)
-set (HHSUITE_VERSION_MINOR 0)
+set(HHSUITE_VERSION_MINOR 1)
 set(HHSUITE_VERSION_PATCH 0)
-set (HHSUITE_DATE "15-03-2015")
-
-set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
-
-INSTALL(FILES
-  hhsuite-userguide.pdf
-  LICENSE
-  README
-  PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
-  DESTINATION ./
-)

+include_directories(${CMAKE_BINARY_DIR}/generated)
+include_directories(${PROJECT_BINARY_DIR}/generated)
 include_directories(src)
 include_directories(lib/ffindex/src)

 add_subdirectory(lib/ffindex)
-add_subdirectory(src)
 add_subdirectory(data)
+add_subdirectory(src)
 add_subdirectory(scripts)
-add_subdirectory(test)
-#add_subdirectory(doc)
-

-SET (CPACK_GENERATOR "DEB;TGZ;ZIP;RPM")
-SET (CPACK_DEBIAN_PACKAGE_MAINTAINER "Markus Meier")
+set(CPACK_GENERATOR "DEB;TGZ;ZIP;RPM")
+set(CPACK_DEBIAN_PACKAGE_MAINTAINER "Markus Meier")

 set(CPACK_SOURCE_IGNORE_FILES
-  ".synctex.gz$"
-  ".toc$"
-  ".blg$"
-  ".bbl$"
-  ".aux$"
-  ".log$"
-  ".dvi$"
-  ".out.ps$"
        "/rpm/"
        "^${PROJECT_SOURCE_DIR}/build/"
        "^${PROJECT_SOURCE_DIR}/.git/"
        "^${PROJECT_SOURCE_DIR}/.gitignore"
        "^${PROJECT_SOURCE_DIR}/.gitattributes"
-  "^${PROJECT_SOURCE_DIR}/.gitmodules"
-  "^${PROJECT_SOURCE_DIR}/.pydevproject"
-  "^${PROJECT_SOURCE_DIR}/.project"
-  "^${PROJECT_SOURCE_DIR}/.cproject"
        "^${PROJECT_SOURCE_DIR}/lib/ffindex/.git"
-  "^${PROJECT_SOURCE_DIR}/lib/ffindex/.git"
-  "^${PROJECT_SOURCE_DIR}/.autotools"
-  "^${PROJECT_SOURCE_DIR}/README.md"
        )

 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
 set(CPACK_PACKAGE_VERSION_MAJOR "${HHSUITE_VERSION_MAJOR}")
 set(CPACK_PACKAGE_VERSION_MINOR "${HHSUITE_VERSION_MINOR}")
 set(CPACK_PACKAGE_VERSION_MINOR "${HHSUITE_VERSION_PATCH}")
-INCLUDE(CPack)
-
-enable_testing()
+include(CPack)
--- a/Dockerfile
+++ b/Dockerfile
+FROM alpine:latest as builder
+
+RUN apk add --no-cache gcc g++ cmake musl-dev vim ninja
+
+WORKDIR /opt/hh-suite
+ADD . .
+
+WORKDIR /opt/hh-suite/build
+RUN cmake -G Ninja -DHAVE_SSE2=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/hh-suite ..
+RUN ninja && ninja install
+
+FROM alpine:latest
+MAINTAINER Milot Mirdita <milot@mirdita.de>
+RUN apk add --no-cache libstdc++ libgomp
+
+COPY --from=builder /usr/local/hh-suite /usr/local/hh-suite
+
+ENV HHLIB=/usr/local/hh-suite
+ENV PATH="/usr/local/hh-suite/bin:/usr/local/hh-suite/scripts:${PATH}"
+
+CMD ["hhblits"]
--- a/LICENSE
+++ b/LICENSE
-
-The hhsuite contains in file hhprefilter.C code adapted from Michael 
-Farrar (http://sites.google.com/site/farrarmichael/smith-waterman). 
-His code is marked in the file hhprefilter.C.
-The copy right of his code is shown below:
-
-Copyright 2006, by Michael Farrar.  All rights reserved. The SWSSE2
-program and documentation may not be sold or incorporated into a
-commercial product, in whole or in part, without written consent of
-Michael Farrar.
-
-For further information regarding permission for use or reproduction, 
-please contact Michael Farrar at:
-
-    farrar.michael@gmail.com
-
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 
-TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-Reference: 
-Farrar M. Striped Smith-Waterman speeds database searches 
-six times over other SIMD implementations. Bioinformatics. 2007, 23:156-61.
-
-Michael Farrar died unexpectedly in December 2010. 
-Many thanks posthumously for your great code!
-
-Johannes
-
-**********************************************************************
-
-
                    GNU GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

@@ -668,8 +631,8 @@ to attach them to the start of each source file to most effectively
 state the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.

-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
+    {one line to give the program's name and a brief idea of what it does.}
+    Copyright (C) {year}  {name of author}

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
@@ -689,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
  If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:

-    <program>  Copyright (C) <year>  <name of author>
+    {project}  Copyright (C) {year}  {fullname}
    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    This is free software, and you are welcome to redistribute it
    under certain conditions; type `show c' for details.

--- a/README
+++ b/README
-*****************************************************************************
-**   HHsuite for sensitive sequence searching version 3.0.0 (15-03-2015)   **
-*****************************************************************************
-
- (C) Johannes Soeding, Markus Meier, Martin Steinegger, Michael Remmert, 
- Andreas Hauser, Andreas Biegert 2015
-
-This README only serves as a quick start guide.
-For full documentation see the user guide in hhsuite-userguide.pdf
-
-
-*****************************************************************************
-1. Requirements
-*****************************************************************************
-
-To compile from source, you will need:
- * a recent C/C++ compiler
- * CMake 2.8.12 or later
- * pdbx python library for example from https://github.com/soedinglab/pdbx
-
-*****************************************************************************
-2. Installation
-*****************************************************************************
-
-We recommend compiling HHsuite on the machine that should run the 
-computations so that it can be optimized for the appropriate CPU architecture.
-
-2.1 Packages
-
-Some distributions incorporate HHsuite on their own:
-* Ubuntu/Debian/etc. [DPKGs](http://packages.debian.org/source/sid/hhsuite) 
-    are provided by Laszlo Kajan.
-* For Archlinux you can find a PKGBUILD on aur 
-    (https://aur.archlinux.org/packages/hhsuite/)
-
-2.2 Release tarballs
- 
-The release tarballs (http://wwwuser.gwdg.de/~compbiol/data/hhsuite/releases/) 
-should contain all required source files. Simply download and extract.
-
-
-2.3 Cloning from GIT
-
-If you want to compile the most recent version, simply clone the git 
-repository. Then, from the repository root, initialize the ffindex submodule:
-
-	git submodule init
-	git submodule update
-
-
-2.3.1 Compilation
-
-With the sourcecode ready, simply run cmake with the default settings and 
-libraries should be auto-detected:
-
-	mkdir build
-	cd build
-	cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" \\ 
-	   -DCMAKE_INSTALL_PREFIX=${INSTALL_BASE_DIR} ..
-	make
-	make install
-
-
-2.3.2 Setting environment variables
-
-In your shell set environment variable HHLIB to ${INSTALL_BASE_DIR}, 
-e.g (for bash, zsh, ksh):
-
-	export HHLIB=${INSTALL_BASE_DIR}
-
-HHsearch and HHblits look for the column state library file cs219.lib
-and the context library file context_data.lib in ${HHLIB}/data/. The HHsuite
-scripts also read HHLIB to locate the perl modules Align.pm and HHPaths.pm 
-in ${HHLIB]/scripts/.  
-
-Add the location of HHsuite binaries and scripts to your search PATH variable
-
-	export PATH=${PATH}:${INSTALL_BASE_DIR}/bin:${INSTALL_BASE_DIR}/scripts
-
-
-2.3.3 Specify BLAST, PSIPRED, PDB, DSSP paths
-
-Specify paths in ${INSTALL_BASE_DIR}/scripts/HHPaths.pm where they are read
-by HHsuite's perl scripts.
-
-
-*****************************************************************************
-3. Download Databases
-*****************************************************************************
-
-Download current databases from our server 
-(http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/)
-To build up multiple sequences alignments using HHblits uniprot20 is sufficient.
-
-
-*****************************************************************************
-4. Usage
-*****************************************************************************
-
-For performing a single search iteration of HHblits, run HHblits with the 
-following command:
-
-	hhblits -i <input-file> -o <result-file> -n 1 -d <database-basename>
-
-For generating an alignment of homologous sequences:
-
-	hhblits -i <input-file> -o <result-file> -oa3m <result-alignment> \\
-	  -d <database-basename>
-
-You can get a detailed list of options for HHblits by running HHblits with 
-the "-h" option.
-
-
-*****************************************************************************
-5. License
-*****************************************************************************
-
-The HHsearch/HHblits software package is distributed under Gnu Public Licence, 
-Version 3. This means that the HH-suite is free software: you can redistribute 
-it and/or modify it under the terms of the GNU General Public License as 
-published by the Free Software Foundation, either version 3 of the License, 
-or (at your option) any later version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT 
-ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-See the copy of the GNU General Public License in the LICENSE file. 
-If you do not have this file, see http://www.gnu.org/licenses/
-
-
-*****************************************************************************
-6. Notes
-*****************************************************************************
-
-For full documentation see the user guide in hhsuite-userguide.pdf
-
-We are very grateful for bug reports! 
-Please contact us at soeding@mpibpc.mpg.de
-
-
-*****************************************************************************
-7. Acknowledgements
-*****************************************************************************
-
-The hhsuite contains in file hhprefilter.cpp code adapted from Michael 
-Farrar (http://sites.google.com/site/farrarmichael/smith-waterman). 
-His code is marked in the file hhprefilter.cpp. For the copy right of that 
-code, please see the LICENSE file that comes with HHsuite.
-Reference: Farrar M. Striped Smith-Waterman speeds database searches six 
-times over other SIMD implementations. Bioinformatics. 2007, 23:156-61.
-Many posthumous thanks to Michael Farrar for his great code!
--- a/README.md
+++ b/README.md
-# Beta-Test
+# HH-suite3 for sensitive sequence searching

-# HHsuite for sensitive sequence searching version 3.0.0 (15-03-2015)
+(C) Johannes Soeding, Markus Meier, Martin Steinegger, Milot, Mirdita, Michael Remmert, Andreas Hauser, Andreas Biegert

- (C) Johannes Soeding, Markus Meier, Martin Steinegger, Michael Remmert, Andreas Hauser, Andreas Biegert 2015
- 
-[ ![Codeship Status for soedinglab/hh-suite](https://codeship.com/projects/0936c290-2248-0133-bcb4-52bb0fef976f/status?branch=master)](https://codeship.com/projects/96085)
-
-[ ![Build Status](https://travis-ci.org/soedinglab/hh-suite.svg?branch=master)](https://travis-ci.org/soedinglab/hh-suite)
+[![Travis Build Status](https://travis-ci.org/soedinglab/hh-suite.svg?branch=master)](https://travis-ci.org/soedinglab/hh-suite)[![Codeship Status for soedinglab/hh-suite](https://codeship.com/projects/0936c290-2248-0133-bcb4-52bb0fef976f/status?branch=master)](https://codeship.com/projects/96085)

 The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

-## WARNING ##
-We had to rename our repository for ffindex, so it might be necessary to run the following commands to update the submodule in your clone:
-
-	git pull
-	git submodule deinit
-	git submodule init
-
-
-## Requirements
-
-To compile from source, you will need:
- * a recent C/C++ compiler
- * [CMake](http://cmake.org/) 2.8.12 or later
- * install [pdbx python library](https://github.com/soedinglab/pdbx)
+## Documentation

+We provide an extensive [user guide](https://github.com/soedinglab/hh-suite/wiki) with many usage examples, frequently asked questions and guides to build your own databases. 

 ## Installation
-We recommend compiling HHsuite on the machine that should run the computations so that it can be optimized for the appropriate CPU architecture.
-
-### Packages
-Some distributions incorporate HHsuite on their own:
-* Ubuntu/Debian/etc. [DPKGs](http://packages.debian.org/source/sid/hhsuite) are provided by Laszlo Kajan.
-* For Archlinux you can find a [PKGBUILD on aur](https://aur.archlinux.org/packages/hhsuite/)
-
-### Release tarballs
-The [release tarballs](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/releases/) should contain all required source files. Simply download and extract
-
-### Cloning from GIT
-If you want to compile the most recent version, simply clone the git repository. Then, from the repository root, initialize the ffindex submodule:
-
-	git submodule init
-	git submodule update
-
+We recommend compiling HH-suite on the machine that should run the computations so that it can be optimized for the available CPU instruction sets.

 ### Compilation
-With the sourcecode ready, simply run cmake with the default settings and libraries should be auto-detected:
-
-	mkdir build
-	cd build
-	cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=${INSTALL_BASE_DIR} ..
-	make
-	make install
-
-
-### Setting paths 
-
-#### Setting environment variables
-In your shell set environment variable HHLIB to ${INSTALL\_BASE\_DIR}, e.g (for bash, zsh, ksh):
-
-	export HHLIB=${INSTALL_BASE_DIR}
-
-HHsearch and HHblits look for the column state library file cs219.lib
-and the context library file context_data.lib in ${HHLIB}/data/. The HHsuite
-scripts also read HHLIB to locate the perl modules Align.pm and HHPaths.pm 
-in ${HHLIB]/scripts/.  
-
-Add the location of HHsuite binaries and scripts to your search PATH variable
-
-	export PATH=${PATH}:${INSTALL_BASE_DIR}/bin:${INSTALL_BASE_DIR}/scripts
-
-
-#### Specify BLAST, PSIPRED, PDB, DSSP paths
-
-Specify paths in ${INSTALL\_BASE\_DIR}/scripts/HHPaths.pm where they are read by HHsuite's perl scripts.
+To compile from source, you will need a recent C/C++ compiler (at least GCC 4.8 or Clang 3.6) and [CMake](http://cmake.org/) 2.8.12 or later.

+To download the source code and compile the HH-suite execute the following commands:
+```
+git clone https://github.com/soedinglab/hh-suite.git
+cd hh-suite && mkdir build && cd build
+cmake -DCMAKE_INSTALL_PREFIX=. ..
+make -j 4 && make install
+export PATH="$(pwd)/bin:$(pwd)/scripts:$PATH"
+```

 ### Download Databases
-Download current databases from our [server](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/)
-To build up multiple sequences alignments using HHblits uniprot20 is sufficient.
-
+Download current databases from our [download server](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/).
+To build up multiple sequences alignments using HHblits, the Uniclust30 database is sufficient.

 ## Usage
-For performing a single search iteration of HHblits, run HHblits with the 
-following command:
-
+For performing a single search iteration of HHblits, run HHblits with the following command:
+```
 hhblits -i <input-file> -o <result-file> -n 1 -d <database-basename>
+```

 For generating an alignment of homologous sequences:
-
+```
 hhblits -i <input-file> -o <result-file> -oa3m <result-alignment> -d <database-basename>
+```

-You can get a detailed list of options for HHblits by running HHblits with the "-h" option.
-
-
-## License
+A detailed list of options for HHblits is available by running HHblits with the `-h` parameter.

-The HHsearch/HHblits software package is distributed under Gnu Public Licence, Version 3.
-This means that the HH-suite is free software: you can redistribute it and/or modify it under the
-terms of the GNU General Public License as published by the Free Software Foundation, either
-version 3 of the License, or (at your option) any later version.
+## Reference

-This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
-without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-PURPOSE. See the GNU General Public License for more details.
-
-See the copy of the GNU General Public License in the LICENSE file. 
-If you do not have this file, see http://www.gnu.org/licenses/
-
-
-## Notes
-For full documentation see the user guide in hhsuite-userguide.pdf
-
-
-We are very grateful for bug reports! 
-Please contact us at soeding@mpibpc.mpg.de
+Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019)
+HH-suite3 for fast remote homology detection and deep protein annotation, *bioRxiv*, 560029. [doi: 10.1101/560029](https://doi.org/10.1101/560029)

 ## Links

-* [soeding lab](http://www.mpibpc.mpg.de/soeding)
-* [databases and precompiled hh-suite versions](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/)
-
-
-## Acknowledgements
- 
-The hhsuite contains in file hhprefilter.cpp code adapted from Michael 
-Farrar (http://sites.google.com/site/farrarmichael/smith-waterman). 
-His code is marked in the file hhprefilter.cpp. For the copy right of that 
-code, please see the LICENSE file that comes with HHsuite.
-Reference: Farrar M. Striped Smith-Waterman speeds database searches six 
-times over other SIMD implementations. Bioinformatics. 2007, 23:156-61.
-Many posthumous thanks to Michael Farrar for his great code!
-
+* [Soeding lab](http://www.mpibpc.mpg.de/soeding)
+* [Databases for the HH-suite](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/)
--- a/cmake/ResourceCompiler.cmake
+++ b/cmake/ResourceCompiler.cmake
+set(compile_resource__internal_dir ${CMAKE_CURRENT_LIST_DIR} CACHE INTERNAL "")
+
+find_program(XXD_EXECUTABLE xxd)
+if(NOT XXD_EXECUTABLE)
+    find_program(PERL_EXECUTABLE perl)
+    if(NOT PERL_EXECUTABLE)
+        message(FATAL_ERROR "Neither xxd nor perl found in PATH. xxd is usually contained in your distributions vim-common package!")
+    else()
+        message("-- xxd not found, using xxdi.pl instead")
+        set(XXD_EXECUTABLE "${compile_resource__internal_dir}/xxdi.pl")
+        set(XXD_PARAMS "")
+    endif()
+else()
+    set(XXD_PARAMS -i)
+endif()
+
+find_program(SED_EXECUTABLE sed)
+if(NOT SED_EXECUTABLE)
+    message(FATAL_ERROR "sed not found in path!")
+endif()
+
+function(compile_resource INPUT_FILE OUTPUT_FILE)
+    get_filename_component(INPUT_FILE_NAME ${PROJECT_SOURCE_DIR}/data/${INPUT_FILE} NAME)
+    set(OUTPUT_FILE ${PROJECT_BINARY_DIR}/generated/${INPUT_FILE_NAME}.h PARENT_SCOPE)
+    add_custom_command(OUTPUT ${PROJECT_BINARY_DIR}/generated/${INPUT_FILE_NAME}.h
+            COMMAND mkdir -p ${PROJECT_BINARY_DIR}/generated
+            COMMAND ${XXD_EXECUTABLE} ${XXD_PARAMS} ${INPUT_FILE} > ${PROJECT_BINARY_DIR}/generated/${INPUT_FILE_NAME}.h
+            COMMAND ${SED_EXECUTABLE} 's!unsigned char!static const unsigned char!' < ${PROJECT_BINARY_DIR}/generated/${INPUT_FILE_NAME}.h > ${PROJECT_BINARY_DIR}/generated/${INPUT_FILE_NAME}.h.tmp
+            COMMAND mv -f ${PROJECT_BINARY_DIR}/generated/${INPUT_FILE_NAME}.h.tmp ${PROJECT_BINARY_DIR}/generated/${INPUT_FILE_NAME}.h
+            WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/data/
+            DEPENDS ${PROJECT_SOURCE_DIR}/data/${INPUT_FILE})
+    set_source_files_properties(${PROJECT_BINARY_DIR}/generated/${INPUT_FILE_NAME}.h PROPERTIES GENERATED TRUE)
+endfunction()
--- a/cmake/xxdi.pl
+++ b/cmake/xxdi.pl
+#!/usr/bin/env perl
+#
+# xxdi.pl - perl implementation of 'xxd -i' mode
+#
+# Copyright 2013 Greg Kroah-Hartman <gregkh@linuxfoundation.org>
+# Copyright 2013 Linux Foundation
+#
+# Released under the GPLv2.
+#
+# Implements the "basic" functionality of 'xxd -i' in perl to keep build
+# systems from having to build/install/rely on vim-core, which not all
+# distros want to do.  But everyone has perl, so use it instead.
+#
+
+use strict;
+use warnings;
+sub slurp {
+    my $file = shift;
+    open my $fh, '<', $file or die;
+    local $/ = undef;
+    my $cont = <$fh>;
+    close $fh;
+    return $cont;
+}
+my $indata = slurp(@ARGV ? $ARGV[0] : \*STDIN);
+my $len_data = length($indata);
+my $num_digits_per_line = 12;
+my $var_name;
+my $outdata;
+
+# Use the variable name of the file we read from, converting '/' and '.
+# to '_', or, if this is stdin, just use "stdin" as the name.
+if (@ARGV) {
+	$var_name = $ARGV[0];
+	$var_name =~ s/\//_/g;
+	$var_name =~ s/\./_/g;
+} else {
+	$var_name = "stdin";
+}
+
+$outdata .= "unsigned char $var_name\[] = {";
+
+# trailing ',' is acceptable, so instead of duplicating the logic for
+# just the last character, live with the extra ','.
+for (my $key= 0; $key < $len_data; $key++) {
+	if ($key % $num_digits_per_line == 0) {
+		$outdata .= "\n\t";
+	}
+	$outdata .= sprintf("0x%.2x, ", ord(substr($indata, $key, 1)));
+}
+
+$outdata .= "\n};\nunsigned int $var_name\_len = $len_data;\n";
+
+binmode STDOUT;
+print {*STDOUT} $outdata;
+
--- a/data/CMakeLists.txt
+++ b/data/CMakeLists.txt
-
-
 INSTALL(FILES
        context_data.crf
        context_data.lib
@@ -11,3 +9,18 @@ INSTALL(FILES
        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
        DESTINATION data
        )
+
+include(ResourceCompiler)
+set(COMPILED_RESOURCES
+        context_data.crf
+        context_data.lib
+        cs219.lib
+        )
+
+set(GENERATED_OUTPUT_HEADERS "")
+FOREACH(INPUT_FILE ${COMPILED_RESOURCES})
+    compile_resource(${INPUT_FILE} OUTPUT_FILE)
+    list(APPEND GENERATED_OUTPUT_HEADERS "${OUTPUT_FILE}")
+ENDFOREACH()
+
+add_custom_target(generated ALL DEPENDS ${GENERATED_OUTPUT_HEADERS})
--- a/data/test.sh
+++ b/data/test.sh
+#!/bin/bash -e
+
+rm -f single* search_* blits_*
+
+hhalign -i query.a3m -t query.a3m
+
+ffindex_build -s single.ffdata single.ffindex query.a3m
+
+mpirun -np 2 \
+    ffindex_apply_mpi single.ffdata single.ffindex -d single_a3m_cons.ffdata -i single_a3m_cons.ffindex \
+        -- hhconsensus -i stdin -oa3m stdout -M a3m -v 0
+
+mpirun -np 2 \
+    ffindex_apply_mpi single_a3m_cons.ffdata single_a3m_cons.ffindex -d single_a3m.ffdata -i single_a3m.ffindex \
+        -- hhfilter -i stdin -o stdout -diff 1000 -v 0
+
+mpirun -np 2 \
+    ffindex_apply_mpi single_a3m.ffdata single_a3m.ffindex -d single_hhm.ffdata -i single_hhm.ffindex \
+        -- hhmake -i stdin -o stdout -v 0
+
+mpirun -np 2 cstranslate_mpi -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m
+
+hhblits -i query.a3m -d single -blasttab blits_app_res -n 1
+hhblits_omp -i single -d single -blasttab blits_omp_res -n 1
+mpirun -np 2 hhblits_mpi -i single -d single -blasttab blits_mpi_res -n 1
+
+diff <(tr -d '\000' < blits_omp_res.ffdata) blits_app_res
+diff <(tr -d '\000' < blits_mpi_res.ffdata) blits_app_res
+
+hhsearch -i query.a3m -d single -blasttab search_app_res
+hhsearch_omp -i single -d single -blasttab search_omp_res
+mpirun -np 2 hhsearch_mpi -i single -d single -blasttab search_mpi_res
+
+diff <(tr -d '\000' < search_omp_res.ffdata) search_app_res
+diff <(tr -d '\000' < search_mpi_res.ffdata) search_app_res
+
+diff <(cut -f 1-10,12 blits_app_res) <(cut -f 1-10,12 search_app_res)
--- a/debian/changelog
+++ b/debian/changelog
+hhsuite (3.1.0-1) UNRELEASED; urgency=medium
+
+  * New upstream release.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 28 Feb 2019 08:16:48 -0600
+
 hhsuite (3.0~beta3+dfsg-3) unstable; urgency=high

  * Team upload

--- a/debian/control
+++ b/debian/control
@@ -44,20 +44,6 @@ Description: sensitive protein sequence searching based on HMM-HMM alignment
 HHblits is faster, up to twice as sensitive and produces more accurate
 alignments.

-Package: hhsuite-doc
-Architecture: all
-Section: doc
-Depends: ${shlibs:Depends},
-         ${misc:Depends}
-Recommends: hhsuite
-Breaks: hhsuite (<= 2.0.16-1)
-Replaces: hhsuite (<= 2.0.16-1)
-Description: documentation for HHsuite for HMM-HMM comparisons
- HH-suite is an open-source software package for sensitive protein sequence
- searching based on the pairwise alignment of hidden Markov models (HMMs).
- .
- This package provides a PDF with the user guide for HH-suite.
-
 Package: hhsuite-data
 Architecture: all
 Depends: ${misc:Depends}

--- a/debian/copyright
+++ b/debian/copyright
@@ -3,7 +3,6 @@ Upstream-Name: hhsuite
 Upstream-Contact: Andreas Hauser <hauser@genzentrum.lmu.de>
                  Johannes Soeding <soeding@genzentrum.lmu.de>
 Source: ftp://toolkit.lmb.uni-muenchen.de/HH-suite/releases/hhsuite-([0-9.]+)\.tar\.gz
-Files-Excluded: hhsuite-userguide.pdf

 Files: *
 Copyright: 2006, 2012 Johannes Soeding

--- a/debian/docs
+++ b/debian/docs
-README
--- a/debian/hhsuite-doc.doc-base
+++ b/debian/hhsuite-doc.doc-base
-Document: hhsuite
-Title: HH-suite User Guide
-Author: Johannes Söding, Michael Remmert, Andreas Hauser
-Abstract: HH-suite for sensitive sequence searching based on HMM-HMM alignment.
-Section: Science/Biology
-
-Format: PDF
-Files: /usr/share/doc/hhsuite/hhsuite-userguide.pdf.gz
--- a/debian/hhsuite-doc.docs
+++ b/debian/hhsuite-doc.docs
-mybuild/doc/hhsuite-userguide.pdf
--- a/debian/hhsuite.docs
+++ b/debian/hhsuite.docs
-README
+README.md